# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  pfam_list/TruD.hmm.txt
# target sequence database:        proteomes/Drosophila_melanogaster.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TruD  [M=416]
Accession:   PF01142.17
Description: tRNA pseudouridine synthase D (TruD)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------               -----------
    9.6e-73  245.0   0.2    7.8e-68  228.8   0.1    3.7  2  tr|Q9VSK9|Q9VSK9_DROME  GH24787p OS=Drosophila melanogaster O


Domain annotation for each sequence (and alignments):
>> tr|Q9VSK9|Q9VSK9_DROME  GH24787p OS=Drosophila melanogaster OX=7227 GN=Dmel\CG6745 PE=1 SV=1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   8.8e-05       1.2      10      34 ..      62      88 ..      52     115 .. 0.70
   2 !  228.8   0.1   5.6e-72   7.8e-68      42     416 .]     235     673 ..     212     673 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 8.8e-05
                    TruD 10 dtegigGrlrespeDFiVeEieef..s 34
                            +++g+ G l+++  DF V+Ei     +
  tr|Q9VSK9|Q9VSK9_DROME 62 EAPGFTGILKSRFSDFHVNEIDSNgkV 88
                            689******************655432 PP

  == domain 2  score: 228.8 bits;  conditional E-value: 5.6e-72
                    TruD  42 geylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlGdLa 126
                              +y+ + v+k+n  t d++++la +l++  ++v+++G+KDkrA TtQ +s+++ +pe++  +  + ++v++ ++g +++ l+lGdL+
  tr|Q9VSK9|Q9VSK9_DROME 235 ADYVTFLVHKTNLVTSDVASTLAARLNLRPSQVNYSGIKDKRAKTTQKFSVKRRTPESILVAarSQRNVHIGNFGFESNTLKLGDLQ 321
                             68999**********************************************999999965444477********************* PP

                    TruD 127 GNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpv.thlvGkaivkgdleeAveayvgkpfeeesedtreare 212
                             GN+F+i +r +a  +e+++++e+ l++lke+g + Ny+G+QRFG+  +v t++vG a++k d++ A e ++ kp +++ e  r +re
  tr|Q9VSK9|Q9VSK9_DROME 322 GNRFRIALRHIA--KEKREEIEQALQSLKERG-FINYYGLQRFGNSASVpTYEVGVALLKHDYKLACE-LILKPRDSDVEFLRPIRE 404
                             **********93..45678***********99.***********8876659*************9986.6789************** PP

                    TruD 213 avaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifa 298
                               ++++d ++a  ++  +  +E+++l+ La+  + dy++Al+++p+n+ +l+ hAyqS +FNr+ s+R+++     + ++GD+v+ +
  tr|Q9VSK9|Q9VSK9_DROME 405 EWWKNRDSAAAAAQIYGEKFIEKKLLDGLARfGESDYSSALRQIPRNMLMLYPHAYQSLIFNRIASRRIKEF-G-LKLIPGDLVYVE 489
                             *******************************8899***********************************98.4.489********* PP

                    TruD 299 eer................................lpdtdrlqlvteknveevkrliergr...afvtaplvGtetelaegevgeie 350
                             +++                                    ++ +++++k     ++ i +g+   + v++pl+G + + ++ e g+  
  tr|Q9VSK9|Q9VSK9_DROME 490 QDQseaseeqaqqgealeeqkeeepndeplevpegDEAIEEESIFKRKVRPLTAEDIASGKyklCDVVLPLPGHDITYPSNECGAWY 576
                             9999*************************99777644445555666666666666776665333789******************** PP

                    TruD 351 revleeegleledFklpklpelsskGtrRaillrve................................dlelsaeedeltleFsLpk 405
                             +e+l+e gl+ ++ k ++ +  + +G++R+++++ +                                 +e++a+   l+leFsLp 
  tr|Q9VSK9|Q9VSK9_DROME 577 EEMLAEVGLSSDQLKHKE-KTYALAGAYRKMIISSSdlkwsfrmyntpedtliasdwellknipvapePAEAEANYMALLLEFSLPT 662
                             ***************887.8999***********999****************************9985566777788********* PP

                    TruD 406 GsYATvvlrEi 416
                               YAT++lrE+
  tr|Q9VSK9|Q9VSK9_DROME 663 AAYATMFLREL 673
                             *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (416 nodes)
Target sequences:                        13786  (7394964 residues searched)
Passed MSV filter:                       538  (0.0390251); expected 275.7 (0.02)
Passed bias filter:                      269  (0.0195125); expected 275.7 (0.02)
Passed Vit filter:                        23  (0.00166836); expected 13.8 (0.001)
Passed Fwd filter:                         1  (7.25374e-05); expected 0.1 (1e-05)
Initial search space (Z):              13786  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.08
# Mc/sec: 38453.81
//
[ok]